Abstract This project seeks to perform deep pathological phenotyping of frontotemporal dementia (FTD) and motor neuron disease (MND). The rationale for the proposal is that, despite the exploding basic biology of FTD and MND, limited information is available about the strongest biological predictors of neurodegeneration in the brains of patients. Even less is known about mechanisms underlying the striking selective vulnerability seen in FTD and MND or what drives the clinico-anatomical overlap of the two disorders. We will pursue these questions with a focus on TAR DNA-binding of 43 kDA (TDP-43) pathobiology, its relationship to other emerging FTD/MND mechanisms, and its targeting of specific neuronal subtypes within the FTD- and MND-related systems. We will further evaluate the complex neuropathological profile seen in C9ORF72 expansion-related FTD/MND and build datasets equipped to help determine which among the many pathological features in sporadic and C9-FTD/MND represent the strongest predictors of neurodegeneration. Our approach seeks to overcome existing methodological barriers by combining advanced histology, a novel tissue multiplexing platform that allows dozens of protein or RNA markers to be quantified in situ, and single nucleus transcriptomics. We will study patients across the FTD/MND- TDP-43 spectrum, including those with the C9ORF72 expansion, and control subjects. We aim to: (1) Relate TDP-43 pathobiology to nuclear transport defects, cryptic exon incorporation, and DNA damage, (2) Determine the pathological changes most prevalent in vulnerable neurons and regions and most strongly linked to neurodegeneration, and (3) Identify transcriptional signatures of neuronal vulnerability and TDP-43 pathobiology in FTD/MND. Successful completion of the proposed aims would resolve key questions about the human relevance of candidate pathogenic mechanisms in FTD/MND-TDP, enabling more informed prioritization of potential targets for human therapeutic development. The integrated multidimensional data produced would create a deep library for testing new hypotheses as they emerge and for generating new hypotheses. Finally, accomplishing our goals would advance a transformative new histopathological approach to studying neurodegenerative and other complex human diseases.